Skip to content

Spestimator version 0.3.0.235#1719

Merged
erinyoung merged 1 commit into
StaPH-B:masterfrom
RaheelSyedAhmed:spestimator-0.3.0.235
Jun 26, 2026
Merged

Spestimator version 0.3.0.235#1719
erinyoung merged 1 commit into
StaPH-B:masterfrom
RaheelSyedAhmed:spestimator-0.3.0.235

Conversation

@RaheelSyedAhmed

Copy link
Copy Markdown
Contributor

Pull Request (PR) checklist:

  • Include a description of what is in this pull request in this message.
  • The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/build-files/samtools/1.15 )
  • Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number in build-files (i.e. docker-builds/build-files/spades/3.12.0/Dockerfile)
    • (optional) All test files are located in same directory as the Dockerfile (i.e. build-files/shigatyper/2.0.1/test.sh)
  • Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. docker-builds/build-files/spades/3.12.0/README.md)
    • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
  • Dockerfile includes the recommended LABELS
  • Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
  • Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

PR Description:
Updated SOFTWARENAME_VER to be SPESTIMATOR_VER=0.3.0.235. The main README.md has been updated to include version 0.3.0.235 in the versions dropdown for spestimator. The program specific README.md is maintained from the prior version; no changes other than a updated 16S database have been made according to the release notes. The program license is still MIT licensed.

…ADME.md has been updated to include version 0.3.0.235 in the versions dropdown for spestimator. The program specific README.md is maintained from the prior version; no changes other than a updated 16S database have been made according to the release notes. The program license is still MIT licensed.
@erinyoung

Copy link
Copy Markdown
Contributor

@staphb-dockerbuilds-diff spestimator 0.3.0.234 0.3.0.235

@github-actions

Copy link
Copy Markdown

Dockerfile Diff: spestimator

Comparing: 0.3.0.234 -> 0.3.0.235

--- build-files/spestimator/0.3.0.234/Dockerfile	2026-06-26 18:45:25.052394917 +0000
+++ build-files/spestimator/0.3.0.235/Dockerfile	2026-06-26 18:45:25.052508459 +0000
@@ -1,11 +1,11 @@
 FROM ubuntu:noble AS app
 
-ARG SOFTWARENAME_VER="0.3.0.234"
+ARG SPESTIMATOR_VER="0.3.0.235"
 
 LABEL base.image="ubuntu:noble"
 LABEL dockerfile.version="1"
 LABEL software="Spestimator"
-LABEL software.version="${SOFTWARENAME_VER}"
+LABEL software.version="${SPESTIMATOR_VER}"
 LABEL description="Uses 16S to identify a range of possible species."
 LABEL website="https://github.com/erinyoung/Spestimator"
 LABEL license="https://github.com/erinyoung/Spestimator/blob/main/LICENSE"
@@ -19,7 +19,7 @@
     python3-pip && \
     apt-get autoclean && rm -rf /var/lib/apt/lists/*
 
-RUN pip install --no-cache-dir --break-system-packages spestimator==${SOFTWARENAME_VER} && \
+RUN pip install --no-cache-dir --break-system-packages spestimator==${SPESTIMATOR_VER} && \
     spestimator -h && \
     mkdir /data
 

@erinyoung

Copy link
Copy Markdown
Contributor

Tests worked

#12 1.613 Volumes:
#12 1.613 	/usr/local/lib/python3.12/dist-packages/spestimator/data/bacteria.16SrRNA
#12 1.613 21:59:41 - Processing 1 input files...
#12 4.922 21:59:44 - File: GCF_900636985.1_45889_C01_genomic.fna -> Top Hit: Klebsiella pasteurii (1 reads)
#12 4.922 21:59:44 - Loading metadata from /usr/local/lib/python3.12/dist-packages/spestimator/data/metadata.csv.gz...
#12 5.029 21:59:45 - Metadata merged successfully.
#12 5.033 21:59:45 - Results saved to testing.csv
#12 5.033 21:59:45 - --- Starting Genome Downloads ---
#12 5.033 21:59:45 - Downloading 9 genomes using NCBI Client...
#12 5.950 21:59:45 - Successfully downloaded and extracted 9 genomes.
#12 6.140 input file,sacc,organism,refseq_assembly_accession,taxid,species_taxid,count,total_bitscore,avg_bitscore,avg_pident,max_pident,avg_qcov,best_evalue
#12 6.140 GCF_900636985.1_45889_C01_genomic.fna,NR_180640,Klebsiella pasteurii,GCF_018139045.1,2587529,2587529,1,22158,2769.75,99.123875,99.351,0.026306068115133516,0.0
#12 6.140 GCF_900636985.1_45889_C01_genomic.fna,NR_118853,Klebsiella oxytoca,GCF_900636985.1,571,571,1,21951,2743.875,99.633875,99.867,0.02564030779294649,0.0
#12 6.140 GCF_900636985.1_45889_C01_genomic.fna,NR_184601,Huaxiibacter chinensis,GCF_022171985.1,2899785,2899785,1,21765,2720.625,98.63275,98.828,0.026220714227673643,0.0
#12 6.140 GCF_900636985.1_45889_C01_genomic.fna,NR_180237,Enterobacter chuandaensis,GCF_039718975.1,2497875,2497875,1,21480,2685.0,98.38025,98.56,0.02608414800773784,0.0
#12 6.140 GCF_900636985.1_45889_C01_genomic.fna,NR_179968,Lelliottia aquatilis,GCF_016771845.1,2080838,2080838,1,21455,2681.875,98.177,98.307,0.026220714227673643,0.0
#12 6.140 GCF_900636985.1_45889_C01_genomic.fna,NR_104934,Yokenella regensburgei,GCF_003634235.1,158877,158877,1,21453,2681.625,98.363625,98.429,0.02608414800773784,0.0
#12 6.140 GCF_900636985.1_45889_C01_genomic.fna,NR_114152,Klebsiella oxytoca,GCF_900636985.1,571,571,1,21437,2679.625,99.607375,99.795,0.02500868902574341,0.0
#12 6.140 GCF_900636985.1_45889_C01_genomic.fna,NR_028688,Citrobacter murliniae,GCF_004801125.1,67829,67829,1,21392,2674.0,98.250375,98.496,0.026101218785229814,0.0
#12 6.140 GCF_900636985.1_45889_C01_genomic.fna,NR_102493,Klebsiella aerogenes KCTC 2190,GCF_019048125.1,1028307,548,1,21392,2674.0,98.00325000000001,98.247,0.02628899733764154,0.0
#12 6.142 9

@erinyoung erinyoung left a comment

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I have no changes to recommend. Thank you for putting this together!

@erinyoung erinyoung merged commit 62bdad6 into StaPH-B:master Jun 26, 2026
2 checks passed
@erinyoung

Copy link
Copy Markdown
Contributor

Thank you for putting this together! You can check the status of the deploy here : https://github.com/StaPH-B/docker-builds/actions/runs/28259127847

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants